Versions and Availability

Softenv Keys for lapack on oliver

▶ Softenv FAQ?

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Softenv

SoftEnv is a utility that is supposed to help users manage complex
user environments with potentially conflicting application versions
and libraries.

System Default Path

When a user logs in, the system /etc/profile
or /etc/csh.cshrc (depending on login shell, and mirrored
from csm:/cfmroot/etc/profile)
calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to
set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the
variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of
available packages. The listing will look something like:

Managing SoftEnv

The file ~/.soft in the user's home directory is where
the different packages are managed. Add the +keyword into your .soft
file. For instance, ff one wants to add the Amber Molecular Dynamics
package into their environment, the end of the .soft file should look
like this:

+amber-8

@default

To update the environment after modifying this file, one simply
uses the resoft command:

% resoft

The command soft can be used to manipulate the environment
from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user
to pay attention to possible order dependencies. That is, best results
require the user to remove keywords in the reverse order in which they
were added. It is handy to test out individual keys, but can lead to
trouble if changing multiple keys. Changing the .soft file and
issuing the resoft is the recommended way of dealing with
multiple changes.

Usage

LAPACK is a binary library, so it is linked to your program by the
compiler during the build process by adding the -llapack
flag to the link line:

Build and Execute

C

The LAPACK routines must be declared with extern,
the routine name must be in lowercase, and it must be followed by
an _ (i.e. underscore):

extern void dgetrf_(int*, int*, double*, int*, int*, int*);

Be sure when calling the LAPACK routing that all arguments
are passed by reference.

Note:Since C matrices are stored in row major order,
and Fortran matrices are stored in column major order, a transpose
is necessary to go from C to Fortran order, and the result transposed
again from Fortran to C order. It is more efficient to change the
array indexing to take this into account.

Build and Execute

C++

The LAPACK routines must be declared with extern
"C", the routine name must be in lowercase, and it must
be followed by an _ (i.e. underscore):

extern "C" void dgetrf_(int*, int*, double*, int*, int*, int*);

Be sure when calling the LAPACK routing that all arguments
are passed by reference.

Note:Since C++ matrices are stored in row major order,
and Fortran matrices are stored in column major order, a transpose
is necessary to go from C to Fortran order, and the result transposed
again from Fortran to C order. It is more efficient to change the
array indexing to take this into account.